Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.

Phytochromes are photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of an embedded chromophore, which triggers a large conformational change in the structure of the entire protein. Although phytochromes have been subject of numerous studies, the photoisomerization mechanism and the following reaction path leading to the final active state remain elusive. Here, we use an integrated computational approach that combines non-adiabatic surface hopping and adiabatic ground-state molecular dynamics simulations to gain atomistic details on the photoactivation mechanism of Deinococcus radiodurans bacteriophytochrome. Our simulations show that the ps-scale photoisomerization of the chromophore proceeds through a hula-twist mechanism that forces a counterclockwise rotation of the D-ring. The initial photoproduct rapidly evolves in an early intermediate which we characterize through IR spectroscopy simulation. The early intermediate then evolves on the nanosecond-to-microsecond scale to a late intermediate, characterized by a more disordered binding pocket and a clear weakening of the aspartate-to-arginine salt bridge interaction, whose cleavage is essential to interconvert to the final active state.

Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded bilin chromophore, which triggers a large conformational change in the protein. The initial photoisomerization and the following structural changes propagating from the chromophore to the entire protein are controlled by a delicate interplay of interactions between the chromophore and the protein residues. Although the numerous studies, the molecular details of this control remain elusive. Here, we apply an integrated computational approach that combines non-adiabatic and adiabatic molecular dynamics simulations to the Deinococcus radiodurans bacteriophytochrome. Our simulations show that the photoisomerization of the chromophore proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen-bonding interaction of the chromophore with a close-by histidine. The resulting photoproduct rapidly relaxes in an early intermediate thanks to a stabilizing effect of a tyrosine, and finally evolves into a late intermediate, characterized by a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the final active state.